Recent advances in developing accurate, physics‐based models of the coupled ionosphere‐thermosphere (CIT) system have now made these models an integral part of next‐generation space weather prediction capabilities. These advances have produced a better understanding of how the CIT is affected by variability in the neutral lower atmosphere. However, the impacts on the CIT of lower atmospheric variability over time scales with characteristic periods longer than ~10 days have received little attention, despite clear evidence of this variability in atmospheric circulation patterns throughout the stratosphere, mesosphere, and lower thermosphere. This review synthesizes the state of knowledge on long‐term variability (>10 days) originating in the lower atmosphere and its impacts on the CIT, highlighting the following critical points and challenges: (a) planetary wave oscillations are likely to couple the lower and upper atmospheres, especially those corresponding to normal modes of the atmosphere, but it remains unclear whether they impact the ionosphere directly via wind‐dynamo coupling, or indirectly via modulation of solar and lunar tides; (b) while fast moving planetary wave oscillations are ubiquitous in the CIT especially during solstices, there is only sporadic evidence that the slowest moving modes are also present in the upper atmosphere; (c) there is abundant evidence of long‐term variations of tidal amplitudes in the CIT, but how and why such variations occur still remain; (d) interseasonal variations associated with major tropospheric and stratospheric variability have been observed, but the physical pathways are still poorly understood. Key Points Large‐scale oscillations with periods longer than 10 days are a potential source of space weather predictability Ionospheric signatures of intraseasonal behavior are ubiquitous, but their origins are poorly understood Observational and modeling studies of pathways linking oscillations from the lower atmosphere to the ionosphere are needed